In a statement to Shacknews from Namco Bandai, a representative for the company said:

It has recently been reported that PAC-MAN & Galaga Dimensionsfor the Nintendo 3DS system lacks an option to erase data that has been saved to the game’s cartridge. I wanted to inform everyone that saved data can be reset by holding the A,B,X,Y,L and R buttons when booting up the game from the 3DS system's home screen. We are sorry for the confusion and hope you enjoy playing PAC-MAN & Galaga Dimensions.

Just last week, Shacknews attempted to confirm and clarify the save file situation for the game. In a long email, the game's QA Lead asserted that saves were permanent and detailed what that decision meant for each game included in the 3DS cart.

Shacknews tested the method that Nacmo Bandai now says will clear the game's data. Upon launching the game while holding down the 3DS' buttons, a menu appears asking whether or not the player wants to delete the data on the cart.